5GJN

Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in P43212 space group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PLK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 400, Sodium citrate, MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.966	α = 90
b = 105.966	β = 90
c = 73.634	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 270		2015-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	50	99	0.073	15.6	11.1		28705

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	100		0.304	0.977		10.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PLK	2	50	27192	1482	99.07	0.2029	0.1958	0.2387	RANDOM	44.354

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.06			1.06		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.948
r_dihedral_angle_4_deg	22.782
r_dihedral_angle_3_deg	14.18
r_dihedral_angle_1_deg	6.685
r_mcangle_it	5.304
r_mcbond_it	4.057
r_mcbond_other	4.057
r_angle_refined_deg	1.921
r_angle_other_deg	1.073
r_chiral_restr	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.948
r_dihedral_angle_4_deg	22.782
r_dihedral_angle_3_deg	14.18
r_dihedral_angle_1_deg	6.685
r_mcangle_it	5.304
r_mcbond_it	4.057
r_mcbond_other	4.057
r_angle_refined_deg	1.921
r_angle_other_deg	1.073
r_chiral_restr	0.116
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2854
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	40

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.